From 42c56d330fdb51820c0fdcbb0b4376ff568ea009 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 18 Oct 2021 12:27:32 +0300
Subject: Move `export_informative` function to `gn3.db.traits` module

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi

* gn3/db/traits.py: Move `export_informative` function here
* gn3/partial_correlations.py: Remove `export_informative` function
* tests/unit/db/test_traits.py: Move `export_informative` function tests here
* tests/unit/test_partial_correlations.py: Remove `export_informative`
  function tests

  The `export_informative` function relates more to the traits than to the
  partial correlations, and could find use in more than just the partial
  correlations stuff. This commit moves the function to the more
  traits-specific `gn3.db.traits` module.
---
 gn3/db/traits.py | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gn3/db')

diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index 1e29aff..1c6aaa7 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -743,3 +743,27 @@ def generate_traits_filename(base_path: str = TMPDIR):
     """Generate a unique filename for use with generated traits files."""
     return "{}/traits_test_file_{}.txt".format(
         os.path.abspath(base_path), random_string(10))
+
+def export_informative(trait_data: dict, inc_var: bool = False) -> tuple:
+    """
+    Export informative strain
+
+    This is a migration of the `exportInformative` function in
+    web/webqtl/base/webqtlTrait.py module in GeneNetwork1.
+
+    There is a chance that the original implementation has a bug, especially
+    dealing with the `inc_var` value. It the `inc_var` value is meant to control
+    the inclusion of the `variance` value, then the current implementation, and
+    that one in GN1 have a bug.
+    """
+    def __exporter__(acc, data_item):
+        if not inc_var or data_item["variance"] is not None:
+            return (
+                acc[0] + (data_item["sample_name"],),
+                acc[1] + (data_item["value"],),
+                acc[2] + (data_item["variance"],))
+        return acc
+    return reduce(
+        __exporter__,
+        filter(lambda td: td["value"] is not None, trait_data["data"].values()),
+        (tuple(), tuple(), tuple()))
-- 
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